Abstract
Genome evolution of bacteria is usually influenced by ecology, such that bacteria with a free-living stage have large genomes and high rates of horizontal gene transfer, while obligate intracellular bacteria have small genomes with typically low amounts of gene exchange. However, recent studies indicate that obligate intracellular species that host-switch frequently harbor agents of horizontal transfer such as mobile elements. For example, the temperate double-stranded DNA bacteriophage WO in Wolbachia persistently transfers between bacterial coinfections in the same host. Here we show that despite the phage's rampant mobility between coinfections, the prophage's genome displays features of constraint related to its intracellular niche. First, there is always at least one intact prophage WO and usually several degenerate, independently-acquired WO prophages in each Wolbachia genome. Second, while the prophage genomes are modular in composition with genes of similar function grouping together, the modules are generally not interchangeable with other unrelated phages and thus do not evolve by the Modular Theory. Third, there is an unusual core genome that strictly consists of head and baseplate genes; other gene modules are frequently deleted. Fourth, the prophage recombinases are diverse and there is no conserved integration sequence. Finally, the molecular evolutionary forces acting on prophage WO are point mutation, intragenic recombination, deletion, and purifying selection. Taken together, these analyses indicate that while lateral transfer of phage WO is pervasive between Wolbachia with occasional new gene uptake, constraints of the intracellular niche obstruct extensive mixture between WO and the global phage population. Although the Modular Theory has long been considered the paradigm of temperate bacteriophage evolution in free-living bacteria, it appears irrelevant in phages of obligate intracellular bacteria.
Highlights
Bacteriophages, viruses that infect bacteria, play a major role in bacterial genome evolution and ecology through their global abundance [1] and their ability to laterally transfer their genomes between bacteria [2,3,4]
To determine the molecular evolutionary forces shaping prophage WO genomes, we addressed four interconnected questions. (i) First, does the Modular Theory explain the genetic changes in WO genomes or do point mutations provide most of the genetic diversity? (ii) Second, does the obligate intracellular niche constrain the acquisition of new genes and/or modules in WO prophages? (iii) Third, is the WO integration site and mechanism conserved in Wolbachia? We explore WO integration by comparing the recombinases encoded in each WO type and the areas of the host Wolbachia genome surrounding the integrated prophages. (iv) what is the relative strength of selection and recombination on prophage WO protein evolution across the functional modules of the genome?
An intact copy of each known structural gene in a Wolbachia genome could allow for bacteriophage protein ‘‘commandeering’’ where the prophages that lack the tail module could use proteins encoded by the other functional haplotype within the genome to complete their assembly and movement
Summary
Bacteriophages, viruses that infect bacteria, play a major role in bacterial genome evolution and ecology through their global abundance [1] and their ability to laterally transfer their genomes between bacteria [2,3,4]. The most common bacterial viruses, the double-stranded (ds)DNA tailed phages, outnumber prokaryotic cells by 10-fold in environmental samples [5] and are responsible for the majority of intraspecific genome diversification in bacteria [6,7,8]. This diversification is due in part to bacteriophages triggering genomic rearrangement in their host bacteria and transmitting new genetic material both within and sometimes between different bacterial species. The Modular Theory of dsDNA phages, as originally proposed by Botstein (1980), asserts that phage genomes consist of conserved clusters of functionally-related genes (i.e. modules) that can be interchanged by horizontal transfer among a large common phage gene pool [14,15]. Obligate intracellular bacteria, which live and replicate within the cytosol of host cells, are an ideal test of the Modular Theory since the intracellular niche may pose ecological restraints on exposure to novel phage gene pools
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